[English] 日本語
Yorodumi- PDB-1iev: CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iev | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH CYCLOHEXITOL | |||||||||
Components | BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 | |||||||||
Keywords | HYDROLASE / 2-domain fold | |||||||||
Function / homology | Function and homology information glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | |||||||||
Biological species | Hordeum vulgare (barley) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Hrmova, M. / DeGori, R. / Fincher, G.B. / Varghese, J.N. | |||||||||
Citation | Journal: Structure / Year: 2001 Title: Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Authors: Hrmova, M. / Varghese, J.N. / De Gori, R. / Smith, B.J. / Driguez, H. / Fincher, G.B. | |||||||||
History |
| |||||||||
Remark 600 | HETEROGEN CONDURITOL B EPOXIDE REACTS WITH THE ENZYME TO FORM A CYCLOHEXITOL RING COVALENTLY BOUND ...HETEROGEN CONDURITOL B EPOXIDE REACTS WITH THE ENZYME TO FORM A CYCLOHEXITOL RING COVALENTLY BOUND TO THE ENZYME. | |||||||||
Remark 999 | SEQUENCE The sequence in the GenBank entry might be a sequencing error at residue 345. The electron ...SEQUENCE The sequence in the GenBank entry might be a sequencing error at residue 345. The electron density unambiguously proved the presence of LYS instead of ASN at this residue. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iev.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iev.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 1iev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iev_validation.pdf.gz | 508.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1iev_full_validation.pdf.gz | 533.8 KB | Display | |
Data in XML | 1iev_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1iev_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1iev ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1iev | HTTPS FTP |
-Related structure data
Related structure data | 1ieqC 1iewC 1iexC 1ex1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer constructed from an (alpha/beta)8 barrel and an (alpha/beta)6 sandwich. |
-Components
#1: Protein | Mass: 65475.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Strain: CULTIVAR CLIPPER References: GenBank: 4566505, UniProt: Q9XEI3*PLUS, glucan 1,3-beta-glucosidase |
---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-INS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.2 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, PEG 400, sodium acetate, Hepes-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277-279 K / Details: Hrmova, M., (1998) Acta Cryst., D54, 687. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 20, 1998 / Details: Monocapillary |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→12 Å / Num. all: 91211 / Num. obs: 19994 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.56 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.8→2.93 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1 / % possible all: 50.8 |
Reflection | *PLUS Num. measured all: 91211 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EX1 Resolution: 2.8→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.1802 / Rfactor Rfree: 0.2401 / Rfactor Rwork: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|